D3b CBTN Summit Workshop
CBTN Multi-Omic Subtyping
This repo provides the necessary setup and analysis scripts to demonstrate the use of CBTN data for multi-omic clustering within the Cavatica Cloud Environment.
In this workshop, we will perform the following:
- Open a new cloud-based RStudio instance within Cavatica's Data Studio
- Clone the d3b-cbtn-summit github repository using the terminal within RStudio
- Review the modules within the repository and their key functionality.
- Prepare epigenomic, transcriptomic, and alternatively splice transcriptome data for high-grade astrocytomas (HGATs) as input to multi-omic clustering.
- Run intNMF matrix factorization for multi-omic clustering using the three data layers outlined in (4).
- Evaluate novel subtypes in relation to known disease subtypes and survival characteristics.
- Evaluate cluster-specific differential expression patterns.
- Time permitting, evaluate cluster-specific differential methylation and differentially methylated pathways.